id

Usage    - print $relationship->id() or $relationship->id($id)
Returns  - the relationship ID (string)
Args     - the relationship ID (string)
Function - gets/sets an ID

type

Usage    - $relationship->type('is_a') or print $relationship->type()
Returns  - the type of the relationship (string)
Args     - the type of the relationship (string)
Function - gets/sets the type of the relationship
Remark   - this field corresponds to the relationship type ID (c.f. OBO::Core::RelationshipType::id())

equals

Usage    - print $relationship->equals($another_relationship)
Returns  - either 1 (true) or 0 (false)
Args     - the relationship (OBO::Core::Relationship) to compare with
Function - tells whether this relationship is equal to the parameter

head

Usage    - $relationship->head($object) or $relationship->head()
Returns  - the OBO::Core::Term (object or target) or OBO::Core::RelationshipType (object or target) targeted by this relationship
Args     - the target term (OBO::Core::Term) or the target relationship type (OBO::Core::RelationshipType)
Function - gets/sets the term/relationship type attached to the head of the relationship

tail

Usage    - $relationship->tail($subject) or $relationship->tail()
Returns  - the OBO::Core::Term (subject or source) or OBO::Core::RelationshipType (subject or source) sourced by this relationship or the OBO::Core::Instance (subject or source)
Args     - the source term (OBO::Core::Term) or the source relationship type (OBO::Core::RelationshipType) or the source instance (OBO::Core::Instance)
Function - gets/sets the term/relationship type/instance attached to the tail of the relationship

link

Usage    - $relationship->link($tail, $head) or $relationship->link()
Returns  - the two Terms (OBO::Core::Term) or two RelationshipTypes (OBO::Core::RelationshipType) or an Instance (OBO::Core::Instance) and a Term (OBO::Core::Term) --subject and source-- connected by this relationship
Args     - the source (tail, OBO::Core::Term/OBO::Core::RelationshipType) and target(head, OBO::Core::Term/OBO::Core::RelationshipType) term/relationship type
Function - gets/sets the terms/relationship type attached to this relationship

NAME

OBO::Core::Relationship - A relationship between two terms or two relationships or an instance and a term within an ontology.

A relationship is simply a triplet: tail->type->head or subject->predicate->object

    SUBJECT                 -->         PREDICATE           -->      OBJECT

OBO::Core::Term             --> OBO::Core::RelationshipType --> OBO::Core::Term
OBO::Core::RelationshipType --> OBO::Core::RelationshipType --> OBO::Core::RelationshipType
OBO::Core::Instance         --> OBO::Core::RelationshipType --> OBO::Core::Term
OBO::Core::Term             --> OBO::Core::RelationshipType --> OBO::Core::Instance
OBO::Core::Term             --> OBO::Core::RelationshipType --> OBO::Core::Datatype (NOT IMPLEMENTED YET)
OBO::Core::Instance         --> OBO::Core::RelationshipType --> OBO::Core::Datatype (NOT IMPLEMENTED YET)

SYNOPSIS

use OBO::Core::Relationship; use OBO::Core::Term; use strict;

# three new relationships my $r1 = OBO::Core::Relationship->new(); my $r2 = OBO::Core::Relationship->new(); my $r3 = OBO::Core::Relationship->new();

$r1->id("APO:P0000001_is_a_APO:P0000002"); $r2->id("APO:P0000002_part_of_APO:P0000003"); $r3->id("APO:P0000001_has_child_APO:P0000003");

$r1->type('is_a'); $r2->type('part_of'); $r3->type('has_child');

!$r1->equals($r2); !$r2->equals($r3); !$r3->equals($r1);

# three new terms my $n1 = OBO::Core::Term->new(); my $n2 = OBO::Core::Term->new(); my $n3 = OBO::Core::Term->new();

$n1->id("APO:P0000001"); $n2->id("APO:P0000002"); $n3->id("APO:P0000003");

$n1->name("One"); $n2->name("Two"); $n3->name("Three");

# r1(n1, n2) $r1->head($n2); $r1->tail($n1);

# r2(n2, n3) $r2->head($n3); $r2->tail($n2);

# r3(n1, n3) $r3->head($n3); $r3->tail($n1);

# three new relationships my $r4 = OBO::Core::Relationship->new(); my $r5 = OBO::Core::Relationship->new(); my $r6 = OBO::Core::Relationship->new();

$r4->id("APO:R0000004"); $r5->id("APO:R0000005"); $r6->id("APO:R0000006");

$r4->type("r4"); $r5->type("r5"); $r6->type("r6");

$r4->link($n1, $n2); $r5->link($n2, $n3); $r6->link($n1, $n3);

DESCRIPTION

A relationship between:

- two Terms (OBO::Core::Term) or - two RelationshipTypes (OBO::Core::RelationshipType) or - an Instance (OBO::Core::Instance) and a Term (OBO::Core::Term)

OBO::Core::Term or OBO::Core::RelationshipType or OBO::Core::Term (1) ^^ ^^ ^^ || || || OBO::Core::Term or OBO::Core::RelationshipType or OBO::Core::Instance (1)

Relationships must have a unique ID (e.g. 'APO:P0000028_is_a_APO:P0000005'), a type (e.g. 'is_a') and it must known the linking terms (tail and head).

AUTHOR

Erick Antezana, <erick.antezana -@- gmail.com>

COPYRIGHT AND LICENSE

Copyright (c) 2006-2015 by Erick Antezana. All rights reserved.

This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself, either Perl version 5.8.7 or, at your option, any later version of Perl 5 you may have available.

cpanm OBO::Util::Set

perl -MCPAN -e shell
install OBO::Util::Set